Cheat sheet: Difference between revisions

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1. Open a terminal and position it on the left side of your screen.

1. Open a terminal and position it on the left side of your screen. If you work with HDF5 data: <code>export NEGGIA_PATH= /usr/local/lib64/dectris-neggia.so</code>. For HDF5 data from Diamond, use <code>export DURIN_PATH= /usr/local/lib64/durin-plugin.so</code> instead (the path must match YOUR computer; the path given is just a typical one).

If you work with HDF5 data: <code>export NEGGIA_PATH= /usr/local/lib64/dectris-neggia.so</code>. For HDF5 data from Diamond, use <code>export DURIN_PATH= /usr/local/lib64/durin-plugin.so</code>instead (the path must match YOUR computer; the path given is just a typical one).

Type <code>xdsgui</code> and move its window so that you still see the left half of the terminal window.

|Keeping the terminal window to the left of the XDSGUI window makes it possible to see e.g. error messages from XDSGUI, or the <code>pointless</code> output. The path to the HDF5 library must appear in "Generic frame library" under <code>xdsgui / Preferences ../ Paths</code> on macOS, or <code>Menu / Settings / Paths</code> on Linux, and should appear after LIB= in <code>XDS.INP</code> (below). Optional: before typing <code>xdsgui</code>: <code>cd</code> to an existing XDS directory, or create a new (empty) directory:<code>cd <toplevel-directory></code>; <code>mkdir <xds-directory>; cd <xds-directory></code>

Type <code>xdsgui</code> and move its window so that you still see the left half of the terminal window.

|Keeping the terminal window to the left of the XDSGUI window makes it possible to see e.g. error messages from XDSGUI, or the <code>pointless</code> output. The path to the HDF5 library must appear in "Generic frame library" under <code>xdsgui / Preferences ../ Paths</code> on macOS, or <code>Menu / Settings / Paths</code> on Linux, and should appear after LIB= in <code>XDS.INP</code> (below). Optional: before typing <code>xdsgui</code>: <code>cd</code> to an existing XDS directory, or create a new (empty) directory:<code>cd <toplevel-directory></code>;<code>mkdir <xds-directory>; cd <xds-directory></code>

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|2. Go to the <code>Projects</code> tab and either 1) choose an existing entry (if there is a list of previous projects), or 2) browse to an existing XDS directory, or 3) create a new (empty) directory

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|The paradigm of manual processing is to repeat INTEGRATE and CORRECT with optimized parameters that are available after a completed XDS run. Please note that geometry parameters for INTEGRATE are in <code>XPARM.XDS</code>, not in <code>XDS.INP</code> !

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|6. Run XDS<~~/small~~>

|6. Run XDS: after changing <code>XDS.INP</code>, click <code>Save</code> (unless greyed out) and <code>Run XDS</code> . The tasks of the JOB keyword are run one after the other. Thus watch the adjacent tabs to the right flash yellow as they are being filled with text and graphics. Inspect the left (text) and right (graphics) sides of these tabs. Once the CORRECT tab is filled, the XDS run has completed, and the reflection file XDS_ASCII.HKL is available. The goal is to make sure that spacegroup and resolution are correct or at least reasonable, and that the processing is optimal.

<~~small~~>click <code>Save</code> (unless greyed out) and <code>Run XDS</code> . The tasks of the JOB keyword are run one after the other. Thus watch the adjacent tabs to the right flash yellow as they are being filled with text and graphics. Inspect the left (text) and right (graphics) sides of these tabs. Once the CORRECT tab is filled, the XDS run has completed, and the reflection file XDS_ASCII.HKL is available. The goal is to make sure that spacegroup and resolution are correct or at least reasonable, and that the processing is optimal.

|If XDS stops after the IDXREF step (with ERROR in IDXREF.LP), this most often happens because it could index less than 50% of the spots only. This may be due to ice rings that obviously cannot be indexed, or due to additional lattices. In most cases, this should at least prompt you to think about the possible reasons. To continue, set JOB=DEFPIX INTEGRATE CORRECT in the XDS.INP tab, <code>Save</code> and <code>Run XDS</code>.

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-<small>1. Open a terminal and position it on the left side of your screen.</small>
+<small>1. Open a terminal and position it on the left side of your screen. If you work with HDF5 data: <code>export NEGGIA_PATH= /usr/local/lib64/dectris-neggia.so</code>. For HDF5 data from Diamond, use <code>export DURIN_PATH= /usr/local/lib64/durin-plugin.so</code> instead (the path must match YOUR computer; the path given is just a typical one).</small>
-<small>If you work with HDF5 data: <code>export NEGGIA_PATH= /usr/local/lib64/dectris-neggia.so</code>. For HDF5 data from Diamond, use <code>export DURIN_PATH= /usr/local/lib64/durin-plugin.so</code>instead (the path must match YOUR computer; the path given is just a typical one).</small>
+<small>Type <code>xdsgui</code> and move its window so that you still see the left half of the terminal window.</small>
+|<small>Keeping the terminal window to the left of the XDSGUI window makes it possible to see e.g. error messages from XDSGUI,  or the <code>pointless</code> output. The path to the HDF5 library must appear in "Generic frame library" under <code>xdsgui / Preferences ../ Paths</code> on macOS, or <code>Menu / Settings / Paths</code> on Linux, and should appear after LIB= in <code>XDS.INP</code> (below). Optional: before typing <code>xdsgui</code>: <code>cd</code> to an existing XDS directory, or create a new (empty) directory:<code>cd <toplevel-directory></code>; <code>mkdir <xds-directory>; cd <xds-directory></code></small>
-<small>Type <code>xdsgui</code> and move its window so that you still see the left half of the terminal window.</small>
-|<small>Keeping the terminal window to the left of the XDSGUI window makes it possible to see e.g. error messages from XDSGUI,  or the <code>pointless</code> output. The path to the HDF5 library must appear in "Generic frame library" under <code>xdsgui / Preferences ../ Paths</code> on macOS, or <code>Menu / Settings / Paths</code> on Linux, and should appear after LIB= in <code>XDS.INP</code> (below). Optional: before typing <code>xdsgui</code>: <code>cd</code> to an existing XDS directory, or create a new (empty) directory:<code>cd <toplevel-directory></code>;<code>mkdir <xds-directory>; cd <xds-directory></code></small>
 |-
 |<small>2. Go to the <code>Projects</code> tab and either 1) choose an existing entry (if there is a list of previous projects), or 2) browse to an existing XDS directory, or 3) create a new (empty) directory</small>
@@ Line 30: / Line 28: @@
 |<small>The paradigm of manual processing is to repeat INTEGRATE and CORRECT with optimized parameters that are available after a completed XDS run. Please note that  geometry parameters for INTEGRATE are in <code>XPARM.XDS</code>, not in <code>XDS.INP</code> !</small>
 |-
-|<small>6. Run XDS</small>
+|<small>6. Run XDS: after changing <code>XDS.INP</code>, click <code>Save</code> (unless greyed out) and <code>Run XDS</code> . The tasks of the JOB keyword are run one after the other. Thus watch the adjacent tabs to the right flash yellow as they are being filled with text and graphics. Inspect the left (text) and right (graphics) sides of these tabs. Once the CORRECT tab is filled, the XDS run has completed, and the reflection file XDS_ASCII.HKL is available. The goal is to make sure that spacegroup and resolution are correct or at least reasonable, and that the processing is optimal.</small>
-<small>click <code>Save</code> (unless greyed out) and <code>Run XDS</code> . The tasks of the JOB keyword are run one after the other. Thus watch the adjacent tabs to the right flash yellow as they are being filled with text and graphics. Inspect the left (text) and right (graphics) sides of these tabs. Once the CORRECT tab is filled, the XDS run has completed, and the reflection file XDS_ASCII.HKL is available. The goal is to make sure that spacegroup and resolution are correct or at least reasonable, and that the processing is optimal.</small>
 |<small>If XDS stops after the IDXREF step (with ERROR in IDXREF.LP), this most often happens because it could index less than 50% of the spots only. This may be due to ice rings that obviously cannot be indexed, or due to additional lattices. In most cases, this should at least prompt you to think about the possible reasons. To continue, set JOB=DEFPIX INTEGRATE CORRECT in the XDS.INP tab, <code>Save</code> and <code>Run XDS</code>.</small>
 |-